Chemical Calculations Research Articles

Enhanced furfural extraction using neoteric hydrophobic solvents for sustainable biomass recovery and bioenergy applications

The recovery of furfural from hemicellulosic biowastes is important for developing sustainable and renewable energy alternatives to fossil fuels. However, current methods are inefficient and environmentally questionable. To address this issue, this study introduces neoteric hydrophobic solvents, specifically deep eutectic solvents (DESs) and ionic liquids (ILs). Of the 32 solvents tested, thymol:decanoic acid 1:1 (Thy:DecA) DES and trihexyltetradecyl phosphonium bis(trifluoro methylsulfonyl) imide [P14,6,6,6][NTf2] IL were the most effective, with extraction efficiencies of 94.1% and 97.1%, respectively. These solvents outperformed the reference solvent toluene, with an efficiency of 81.2%, while also showing favorable characteristics in multiple investigated criterions. For the first time, excellent performance stability was demonstrated under various operational conditions and reusability over multiple extraction and regeneration cycles. Furthermore, to provide insights into the molecular mechanisms of extraction, computational quantum chemistry modeling was employed, which showed a strong agreement with the experimental results. The development of these new neoteric solvents for furfural recovery from biowaste offers a highly effective, sustainable, and eco-friendly alternative to traditional solvents, representing a significant breakthrough in the field of renewable bioenergy production and sustainable materials recovery.

Conformational Sampling in Computational Studies of Natural Products: Why Is It Important?

Conformational sampling is a vital component of a reliable computational chemistry investigation. With the aim of illustrating the importance of conformational sampling, and building awareness among new practitioners, we present a series of case studies that show how the quality and reliability of computational studies depend on undertaking a thorough conformer search. The examples are drawn from the most common types of research questions in natural products chemistry, but the fundamental principles apply more generally to computational studies of molecular structure and behavior in any field of chemistry.

Assessment of the inhibition performance of ZIF-8 on corrosion Mitigation of API 5L X65 steel in 3.5 wt% NaCl: Experimental and theoretical insight

The synthesis and application of ZIF-8 as an effective corrosion inhibitor for the corrosion of API 5L X65 steel in 3.5 wt% NaCl have been studied. The synthesized ZIF-8 was characterized using some surface probe approaches, which include field emission scanning electron microscopy (FE-SEM), X-ray diffraction (XRD), high-resolution transmission electron microscopy (HR TEM), and X-ray photoelectron spectroscopy (XPS), respectively. The results showed that ZIF-8 exhibited regular hexagonal and orthorhombic-shaped nanoparticles. An approximately 62% yield was achieved. Electrochemical studies such as open circuit potential (OCP), potentiodynamic polarization (PDP), and electrochemical impedance spectroscopy (EIS) were performed. The polarization results show that ZIF-8 is a mixed-type inhibitor, revealing a strong impact on both the anodic and cathodic polarization current values. The EIS studies reveal an increase in the charge transfer resistance upon the introduction of ZIF-8. The existence of a strong protective film adsorbed on X65 steel was recognized via XPS and FT-IR analysis. The highest inhibition efficiency value of 98.1% was recorded at a concentration of 0.120 wt% ZIF-8. Quantum chemical computations in the framework of DFT and molecular dynamic simulation were used to determine the reaction sites on the inhibitor, and as such, in-depth insight into the reaction mechanism was revealed.

Text Mining and Computational Chemistry Reveal Trends in Applications of Laser Desorption/Ionization Techniques to Small Molecules.

Continued development of laser desorption/ionization (LDI) since its inception in the 1960s has produced an explosion of soft ionization techniques, where ionization is assisted by the physical or chemical properties of a structure or matrix. While many of these techniques have primarily been used to ionize large biomolecules, including proteins, some have recently seen increasing applications to small molecules such as pharmaceuticals. Small molecules pose particular challenges for LDI techniques, including interference from the matrix or support in the low mass range. To investigate trends in the application of soft LDI techniques to small molecules, we combined text mining and computational chemistry, looking specifically at matrix substances, analyte properties, and the research domain. In addition to making visible the history of LDI techniques, the results may inform the choice of method and suggest new avenues of method development. All software and collected data are freely available on GitHub (https://github.com/ReinV/SCOPE), VOSviewer (https://www.vosviewer.com), and OSF (https://osf.io/zkmua/).

Development of Highly Sensitive Immunochromatography Using Time-Resolved Fluorescence Microspheres for Amantadine Detection.

Amantadine (AMA), commonly used to treat viral infections in livestock and poultry, has been banned owing to its potential hazards to human well-being. To detect unauthorized AMA usage in livestock, we developed a polyclonal antibody with a high affinity for the specific recognition of AMA through a rational design based on a structure similar to AMA and revealed the availability of the hapten design by computational chemistry analysis. Using this antibody, we established a highly responsive time-resolved fluorescence immunochromatographic assay (TRFICA). The visual detection limit of the assay is 0.6 μg/kg, and the quantitative detection limit is 0.05 μg/kg. The TRFICA also showed good recovery rates ranging from 94.5 to 109.9%, with variability coefficients not exceeding 10%. The outcomes of undisclosed sample examinations aligned with those of HPLC-MS/MS analyses, indicating that this approach can function as an ideal screening and monitoring tool for detecting illegal AMA in chicken muscle.

Solvent-free mechanosynthesis of Schiff bases derived from thiadiazole with potential application in sensing ionic species and NLO applications

In this work, we report the solvent-free mechanosynthesis of three Schiff bases (SBs) derived from 1,3,4-thiadiazole covalently bonded to indole (Th-In), quinoline (Th-Qn) and triphenylamine (Th-TPA) groups. This green chemistry method showed a drastic reduction in reaction time and avoidance of solvents for obtaining SBs, with good reaction yields. The molecular structures of SBs were investigated by computational chemistry calculations, with global reactivity parameters indicative of electron acceptor behavior, estimation of frontier molecular orbitals, and their theoretical band gaps of 3.49 and 3.4 eV for Th-In and Th-Qn, respectively, and the lowest of 299 eV for Th-TPA. To evaluate the possible NLO response, the hyperpolarizabilities (β) were also estimated, which are several orders of magnitude higher than the urea value used as a reference. The absorption and emission spectra were calculated using TD-DFT. These results showed a larger redshift for Th-TPA, with possible charge transfer processes more intense than those obtained for Th-In and Th-Qn. The photophysical properties of the Schiff bases were determined, with band gap values for Th-In, Th-Qn, and Th-TPA of 2.53, 2.66, and 2.39 eV in solution and 2.77, 2.26, and 2.21 eV in film, respectively. When the SBs were evaluated as potential naked-eye colorimetric chemosensors, colorimetric changes were observed in Fe2+, Fe3+, Pb2+, Cu2+, and Ag+ ions, with Ag+ being the most promising. Z-scan was used to evaluate the nonlinear response of the SBs and showed saturable absorber behavior with self-focusing processes. Cyclic voltammetry was used to determine the electrochemical band gaps, which were 2.70, 2.71, and 1.98 eV for Th-In, Th-Qn, and Th-TPA, respectively. Th-TPA exhibits superior optical and electrical properties among the three SBs investigated. In addition, it exhibits photochromism, which can be used in conjunction with its other properties in NLO and sensor applications.

Exploring Ground and Excited States Via Single Reference Coupled-Cluster Theory and Algebraic Geometry.

The exploration of the root structure of coupled cluster (CC) equations holds both foundational and practical significance for computational quantum chemistry. This study provides insight into the intricate root structures of these nonlinear equations at both the CCD and CCSD level of theory. We utilize computational techniques from algebraic geometry, specifically the monodromy and parametric homotopy continuation methods, to calculate the full solution set. We compare the computed CC roots against various established theoretical upper bounds, shedding light on the accuracy and efficiency of these bounds. We hereby focus on the dissociation processes of four-electron systems such as (H2)2 in both D2h and D∞h configurations, H4 symmetrically distorted on a circle, and lithium hydride. We moreover investigate the ability of single-reference CC solutions to approximate excited state energies. We find that multiple CC roots describe energies of excited states with high accuracy. Our investigations reveal that for systems like lithium hydride, CC not only provides high-accuracy approximations to several excited state energies but also to the states themselves.

Physicochemical and structural analysis of N-phenylacetyl-L-prolylglycine ethyl ester (Noopept) – An active pharmaceutical ingredient with nootropic activity

N-Phenylacetyl-L-prolylglycine ethyl ester (Noopept, GVS-111, omberacetam) is an orally available active pharmaceutical ingredient (API), with neuroprotective properties and ability to enhance cognitive function. It belongs to nootropic family of drugs and is included in the group of racetams, although its chemical structure is quite different than the other compounds from this group, including the most popular one – piracetam. The mechanism of action of this API is multifaced and is considered to be involving modulation of various neurotransmitter systems within the brain. Despite the significant amount of works devoted to the pharmacodynamics of Noopept, very little is known about its structural and physicochemical properties. Therefore, the aim of current study was to investigate this API in a very thorough way. In this work, the detailed physicochemical analysis of Noopept has been done using TGA/DSC, 1H and 13C liquid state NMR, 13C CP/MAS NMR, SEM, SCXRD, and PXRD. Additionally, quantum chemical DFT computations under periodic boundary conditions, using CASTEP, were conducted to facilitate the analysis of experimental results. Besides, we’ve performed a polymorphism screening of this molecule.

Rapid and Highly Selective Fe(IV) Generation by Fe(II)-Peroxyacid Advanced Oxidation Processes: Mechanistic Investigation via Kinetics and Density Functional Theory.

High-valent iron (Fe(IV/V/VI)) has been widely applied in water decontamination. However, common Fe(II)-activating oxidants including hydrogen peroxide (H2O2) and persulfate react slowly with Fe(II) and exhibit low selectivity for Fe(IV) production due to the cogeneration of radicals. Herein, we report peroxyacids (POAs; R-C(O)OOH) that can react with Fe(II) more than 3 orders of magnitude faster than H2O2, with high selectivity for Fe(IV) generation. Rapid degradation of bisphenol A (BPA, an endocrine disruptor) was achieved by the combination of Fe(II) with performic acid (PFA), peracetic acid (PAA), or perpropionic acid (PPA) within one second. Experiments with phenyl methyl sulfoxide (PMSO) and tert-butyl alcohol (TBA) revealed Fe(IV) as the major reactive species in all three Fe(II)-POA systems, with a minor contribution of radicals (i.e., •OH and R-C(O)O•). To understand the exceptionally high reactivity of POAs, a detailed computational comparison among the Fenton-like reactions with step-by-step thermodynamic evaluation was conducted. The high reactivity is attributed to the lower energy barriers for O-O bond cleavage, which is determined as the rate-limiting step for the Fenton-like reactions, and the thermodynamically favorable bidentate binding pathway of POA with iron. Overall, this study advances knowledge on POAs as novel Fenton-like reagents and sheds light on computational chemistry for these systems.

Ultrasound‐Assisted Catalysis: A Pathway to Novel and Selective Chemical Transformations in Condensed Phase

AbstractIn this paper, we review the concept of synergistically using ultrasonic sonochemistry in combination with heterogeneous catalysis, to selectively perform condensed phase chemical transformations. Through specific examples, we highlight that ultrasound induced cavitation bubbles not only provide local high temperature and pressure conditions for initiating chemical reactions but also improves heat, mass and charge transfer characteristics in the system. We also show that sonocatalysis can alter reaction mechanisms and open new activation and reaction pathways that are not intuitive to thermocatalysis. Computational chemistry tools are introduced and are combined with sonocatalysis experimental studies to demonstrate that, in‐situ generated radicals propelled into the bulk liquid solution upon bubbles implosion can be stabilized by catalyst surfaces, while creating active sites for unique reactions during heterogeneous sonocatalytic chemistry. We also report recent examples of condensed phase sonocatalysis applications, including pollutant degradation, chemical and pharmaceutical synthesis and biomass upgrading, and provide mechanistic insights into the process.

Laboratory and Computational Studies of Interstellar Ices

Ice mantles play a crucial role in shaping the astrochemical inventory of molecules during star and planet formation. Small-scale molecular processes have a profound impact on large-scale astronomical evolution. The areas of solid-state laboratory astrophysics and computational chemistry involve the study of these processes. We review laboratory efforts in ice spectroscopy, methodological advances and challenges, and laboratory and computational studies of ice physics and ice chemistry. We place the last of these in context with ice evolution from clouds to disks. Three takeaway messages from this review are: ▪Laboratory and computational studies allow interpretation of astronomical ice spectra in terms of identification, ice morphology, and local environmental conditions as well as the formation of the involved chemical compounds.▪A detailed understanding of the underlying processes is needed to build reliable astrochemical models to make predictions about abundances in space.▪The relative importance of the different ice processes studied in the laboratory and computationally changes during the process of star and planet formation.

Extraction and detection of sulfonamide antibiotics in milk using magnetic solid-phase adsorbent based on molecular mechanics and DFT calculations

Based on the foundation of calculations in molecular mechanics and density functional theory (DFT) for in-depth mechanistic studies, this paper proposes the sample multi-residue analysis method of five common sulfonamide antibiotics (SAs) in milk. Fe3O4 nanoparticles modified magnetic graphene oxide nanoribbons (Mag-GONRs) with superior dispersibility and dispersion stability, were developed and firstly utilized to rapidly extract residual SAs from milk. Therefore, various SAs in complex samples could be simultaneously determined solely by high performance liquid chromatography-ultraviolet detector (HPLC-UV) without the need for complicated pretreatment processes. In order to obtain satisfactory extraction efficiency, indispensable investigation and optimization were conducted on some parameters influencing the extraction efficiency. And the extracted SAs were determined by. Good linearity for all analytes was achieved with appropriate correlation coefficients (R2 higher than 0.9978). The limits of detection ranged from 0.060 to 0.075 ng·mL−1. Recoveries of the sulfonamides in spiked milk samples were between 79.6 % and 114.6 %, with relative standard deviations within 12 %. Interestingly, with the assistant of computational chemistry, the efficient extraction of Mag-GONRs onto SAs has been validated at the molecular and quantum levels, further elucidating the adsorption mechanism based on non-covalent interactions. In the context of theoretical research and experimental results mutually supporting each other, a practical detection method with actual application value has been proposed in monitoring the residual sulfonamides in milk by the common devices.

Molecular Simulation Analysis of Polyurethane Molecular Structure under External Electric Field.

Polyurethane (PU) materials are extensively utilized in power equipment. This paper introduces a comprehensive evaluation method that combines electromagnetics and computational chemistry based on the Density Functional Theory (DFT) to elucidate the impact of external electric fields on the molecular structure of PU during electrical contact. The study focuses on the microstructural and molecular energy changes in the hard (HS) and soft (SS) segments of PU under the influence of an electric field of uniform intensity. Findings indicate that the total energy of HS molecules decreases markedly as the electric field intensity increases, accompanied by a significant rise in both the dipole moment and polarizability. Conversely, the total energy and polarizability of the SS molecules decrease, while the dipole moment experiences a slight increase. Under the influence of a strong electric field, HS molecules tend to stretch towards the extremities of the main chain, leading to structural instability and the cleavage of hydroxyl O-H bonds. Meanwhile, the carbon chain of the SS molecules twists towards the center under the electric field, with no chemical bond rupture observed. At an electric field intensity of 8.227 V/nm, the HOMO-LUMO gap of the HS molecule narrows sharply, signifying a rapid decline in the molecular structure stability, corroborated by infrared spectroscopy analysis. These findings offer theoretical insights and guidance for the modification of PU materials in power equipment applications.

Enhanced corrosion inhibition performance of 5-amino-3‑bromo-1-methylindazole on copper in sulfuric acid environments

The corrosion inhibitor 5-amino-3‑bromo-1-methylindazole (ABMI) with multiple substituents can effectively protect the copper substrate. According to the electrochemical experiment results, at 298 K, 3 mM ABMI may suppress copper corrosion by 92.1 %. Furthermore, going from 298 K to 308 K raises the temperature at which 3 mM ABMI may continue to suppress corrosion with an efficiency exceeding 90 %. The weight loss test, SEM, AFM, and XRD data all reveal that the presence of ABMI efficiently prevents the corrosion media from dissolving the copper substrate. The ΔGads0 value of ABMI is −32.97 kJ/mol, demonstrating that it works on the metal/solution interface through physical adsorption and chemisorption. The results of molecular dynamics modeling and quantum chemical computation show that ABMI adsorbs to the metal superficies in a nearly parallel way, minimizing the exposure area among the metal superficies with the medium with corrosive substances and providing the best possible protection for copper.

In-silico screening of Staphylococcus aureus antibacterial agents based on Isatin scaffold: QSAR, molecular docking, molecular dynamics simulation and DFT analysis

The design of novel antimicrobial drugs is necessary due to the increasing resistance to many existing antibiotics. Considering that the drug discovery process requires a lot of time and resources, computational chemistry and molecular docking as the basic components in the drug discovery process, can help the acceleration of this prolonged process and minimise the research costs. In this study, 64 molecules containing the Isatin scaffold were subjected to quantitative structure–activity relationship analysis to identify the necessary features for designing effective antimicrobial agents. Three chemometrics methods were employed to establish a connection between structural parameters and antibacterial effects. MLR was identified as the best model, demonstrating high accuracy compared to the other models. Based on the obtained model, ten novel lead compounds were designed, and their antibacterial potency of these compounds was assessed. The outputs of the molecular docking study revealed that compound S4 fits well in the ATP-binding site and blocks ATPase activity. Additionally, it was observed that compound S4 exhibited adequate binding affinity against the DNA gyrase target. An appropriate relationship was observed between QSAR, DFT and molecular modelling approaches. Therefore, compound S4 can be considered as a promising candidate for further development as an antibacterial agent.

Unmasking Fluorinated Moieties on the Surface of Hydride-Terminated Silicon Nanoparticles.

Despite the widespread use of hydrofluoric acid (HF) in the preparation of silicon surfaces, the true nature of fluorinated surface species remains unclear. Here, we employ an array of characterization techniques led by solid-state nuclear magnetic resonance spectroscopy to uncover the nature of fluorinated moieties on the surface of hydride-terminated silicon nanoparticles (H-SiNPs). A structural model that explains the observed trends in 19F and 29Si magnetic shielding is proposed and further supported by quantum chemical computations. Fluorine is incorporated into local oxidation domains on the surface and clustered at the interface of the oxide and surrounding hydride-terminated surface. Silicon sites capped by a single fluorine are also identified by their distinct 19F and 29Si chemical shifts, providing insight into how fluorine termination influences the electronic structure. The extent of fluorine passivation and the effects of fluorine on the optical properties of SiNPs are also discussed. Finally, challenges associated with Teflon contamination are highlighted that future explorations of nanomaterials may have to contend with.

Vibrational and Rovibrational Spectroscopic Data for the Ground and First-Excited States of Phosgene (COCl2), Formic Acid (HCOOH), and Chloroformic Acid (ClCOOH).

While "black box" quantum chemical computations for the determination of rovibronic spectral data are not quite at hand, the present work utilizes the titular molecules to showcase how excited-state quantum chemical methods can be conjoined to quartic force field (QFF) anharmonic rovibrational treatments to provide novel and useful predictions for such data. This work employs hybrid QFFs with explicitly correlated coupled cluster theory along with the equation-of-motion formalism to generate harmonic force constants and time-dependent density functional theory (TD-DFT) to produce anharmonic force constants for the generation of electronically excited-state rovibrational spectral data, in effect, rovibronic spectral data. Specific spectroscopic results from this work show that the fundamental C═O stretch in phosgene as well as in cis- and trans-formic acid drop from the region of around 1800 cm-1 to close to 1100 cm-1 or less in the first excited states of each molecule. While such is expected for these n → π* excitations, this work provides quantitative predictions for these fundamental vibrational frequencies. The most notable theoretical result is that the TD-DFT-based QFFs can experience unexpected failures, and their inclusion in excited-state hybrid QFFs should require at least two functionals to be employed. The computation of DFT QFFs is relatively fast, and such a "doubling up" of the QFFs will not greatly increase the computational time.

Computational and Experimental Comparison of Molecularly Imprinted Polymers Prepared by Different Functional Monomers-Quantitative Parameters Defined Based on Molecular Dynamics Simulation.

In recent years, the advancement of computational chemistry has offered new insights into the rational design of molecularly imprinted polymers (MIPs). From this aspect, our study tried to give quantitative parameters for evaluating imprinting efficiency and exploring the formation mechanism of MIPs by combining simulation and experiments. The pre-polymerization system of sulfadimethoxine (SDM) was investigated using a combination of quantum chemical (QC) calculations and molecular dynamics (MD) simulations. MIPs were prepared on the surface of silica gel by a surface-initiated supplemental activator and reducing agent atom transfer radical polymerization (SI-SARA ATRP). The results of the QC calculations showed that carboxylic monomers exhibited higher bonding energies with template molecules than carboxylic ester monomers. MD simulations confirmed the hydrogen bonding sites predicted by QC calculations. Furthermore, it was observed that only two molecules of monomers could bind up to one molecule of SDM, even when the functional monomer ratio was up to 10. Two quantitative parameters, namely, the effective binding number (EBN) and the maximum hydrogen bond number (HBNMax), were defined. Higher values of EBN and HBNMax indicated a higher effective binding efficiency. Hydrogen bond occupancies and RDF analysis were performed to analyze the hydrogen bond formation between the template and the monomer from different perspectives. Furthermore, under the influence of the EBN and collision probability of the template and the monomers, the experimental results show that the optimal molar ratio of template to monomer is 1:3. The method of monomer screening presented in this study can be extended to future investigations of pre-polymerization systems involving different templates and monomers.

Massively Parallel Computational Chemistry with the Super Instruction Architecture and ACES4.

The task of developing high-performing parallel software must be made easier and more cost-effective in order to fully exploit existing and emerging large-scale computer systems for the advancement of science. The Super Instruction Architecture (SIA) is a parallel programming platform geared toward applications that need to manage large amounts of data stored in potentially sparse multidimensional arrays during calculations. The SIA platform was originally designed for the quantum chemistry software package ACESIII. More recently, the SIA was reimplemented to overcome the limitations in the original ACESIII program. It has now been successfully employed in the new ACES4 quantum chemistry software package. This paper describes the SIA and ACES4 and illustrates their capabilities with some difficult quantum chemistry open-shell coupled-cluster benchmark calculations.

TIMM9 as a prognostic biomarker in multiple cancers and its associated biological processes

TIMM9 has been identified as a mediator of essential functions in mitochondria, but its association with pan-cancer is poorly understood. We herein employed bioinformatics, computational chemistry techniques and experiments to investigate the role of TIMM9 in pan-cancer. Our analysis revealed that overexpression of TIMM9 was significantly associated with tumorigenesis, pathological stage progression, and metastasis. Missense mutations (particularly the S49L variant), copy number variations (CNV) and methylation alterations in TIMM9 were found to be associated with poor cancer prognosis. Moreover, TIMM9 was positively related with cell cycle progression, mitochondrial and ribosomal function, oxidative phosphorylation, TCA cycle activity, innate and adaptive immunity. Additionally, we discovered that TIMM9 could be regulated by cancer-associated signaling pathways, such as the mTOR pathway. Using molecular simulations, we identified ITFG1 as the protein that has the strongest physical association with TIMM9, which show a promising structural complement.